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HUE058678T2 - Detection of repeat expansions with short read sequencing data - Google Patents

Detection of repeat expansions with short read sequencing data

Info

Publication number
HUE058678T2
HUE058678T2 HUE15771527A HUE15771527A HUE058678T2 HU E058678 T2 HUE058678 T2 HU E058678T2 HU E15771527 A HUE15771527 A HU E15771527A HU E15771527 A HUE15771527 A HU E15771527A HU E058678 T2 HUE058678 T2 HU E058678T2
Authority
HU
Hungary
Prior art keywords
detection
sequencing data
short read
read sequencing
repeat expansions
Prior art date
Application number
HUE15771527A
Other languages
Hungarian (hu)
Inventor
Michael A Eberle
Richard Shaw
Original Assignee
Illumina Cambridge Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Illumina Cambridge Ltd filed Critical Illumina Cambridge Ltd
Publication of HUE058678T2 publication Critical patent/HUE058678T2/en

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
HUE15771527A 2014-09-12 2015-09-11 Detection of repeat expansions with short read sequencing data HUE058678T2 (en)

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
US201462049925P 2014-09-12 2014-09-12

Publications (1)

Publication Number Publication Date
HUE058678T2 true HUE058678T2 (en) 2022-09-28

Family

ID=54207462

Family Applications (1)

Application Number Title Priority Date Filing Date
HUE15771527A HUE058678T2 (en) 2014-09-12 2015-09-11 Detection of repeat expansions with short read sequencing data

Country Status (11)

Country Link
US (2) US10699801B2 (en)
EP (2) EP3191993B1 (en)
CN (2) CN107077537B (en)
AU (3) AU2015314114B2 (en)
DK (1) DK3191993T3 (en)
ES (1) ES2915399T3 (en)
HU (1) HUE058678T2 (en)
LT (1) LT3191993T (en)
PL (1) PL3191993T3 (en)
PT (1) PT3191993T (en)
WO (1) WO2016038220A1 (en)

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US9892230B2 (en) 2012-03-08 2018-02-13 The Chinese University Of Hong Kong Size-based analysis of fetal or tumor DNA fraction in plasma
WO2016008451A1 (en) 2014-07-18 2016-01-21 The Chinese University Of Hong Kong Methylation pattern analysis of tissues in dna mixture
ES2915399T3 (en) * 2014-09-12 2022-06-22 Illumina Cambridge Ltd Detection of repeat expansions with short-read sequencing data
US10364467B2 (en) 2015-01-13 2019-07-30 The Chinese University Of Hong Kong Using size and number aberrations in plasma DNA for detecting cancer
US10395759B2 (en) 2015-05-18 2019-08-27 Regeneron Pharmaceuticals, Inc. Methods and systems for copy number variant detection
HK1259478A1 (en) 2016-02-12 2019-11-29 Regeneron Pharmaceuticals, Inc. Methods and systems for detection of abnormal karyotypes
US10508305B2 (en) 2016-02-28 2019-12-17 Damoun Nashtaali DNA sequencing and processing
WO2018089567A1 (en) * 2016-11-10 2018-05-17 Life Technologies Corporation Methods, systems and computer readable media to correct base calls in repeat regions of nucleic acid sequence reads
AU2017369018B2 (en) 2016-11-30 2021-02-25 The Chinese University Of Hong Kong Analysis of cell-free DNA in urine and other samples
WO2019028189A2 (en) * 2017-08-01 2019-02-07 Human Longevity, Inc. Determination of str length by short read sequencing
TWI695890B (en) * 2017-12-29 2020-06-11 行動基因生技股份有限公司 Method and system for sequence alignment and variant calling
CN119753091A (en) 2018-04-02 2025-04-04 格里尔公司 Assay plate for amplifying cfDNA molecules associated with cancer
EP3856903A4 (en) 2018-09-27 2022-07-27 Grail, LLC METHYLATION MARKERS AND TARGETED METHYLATION PROBE PANELS
CA3114759A1 (en) * 2019-03-07 2020-09-10 Illumina, Inc. Sequence-graph based tool for determining variation in short tandem repeat regions
US11676685B2 (en) 2019-03-21 2023-06-13 Illumina, Inc. Artificial intelligence-based quality scoring
US11210554B2 (en) 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata
US11423306B2 (en) 2019-05-16 2022-08-23 Illumina, Inc. Systems and devices for characterization and performance analysis of pixel-based sequencing
US11593649B2 (en) 2019-05-16 2023-02-28 Illumina, Inc. Base calling using convolutions
GB2626687B (en) 2020-02-05 2024-10-16 Univ Hong Kong Chinese Molecular analyses using long cell-free fragments in pregnancy
US11475981B2 (en) 2020-02-18 2022-10-18 Tempus Labs, Inc. Methods and systems for dynamic variant thresholding in a liquid biopsy assay
US11211147B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Estimation of circulating tumor fraction using off-target reads of targeted-panel sequencing
US11211144B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Methods and systems for refining copy number variation in a liquid biopsy assay
US20210265016A1 (en) 2020-02-20 2021-08-26 Illumina, Inc. Data Compression for Artificial Intelligence-Based Base Calling
IL295560A (en) 2020-02-20 2022-10-01 Illumina Inc An artificial intelligence-based many-to-many base reader
US12354008B2 (en) 2020-02-20 2025-07-08 Illumina, Inc. Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller
US12217829B2 (en) 2021-04-15 2025-02-04 Illumina, Inc. Artificial intelligence-based analysis of protein three-dimensional (3D) structures
US20220336057A1 (en) 2021-04-15 2022-10-20 Illumina, Inc. Efficient voxelization for deep learning
CA3222329A1 (en) * 2021-06-11 2022-12-15 Sai CHEN Determining pathogenic rfc1 expansions from sequencing data
CN114807331B (en) * 2022-05-12 2024-06-18 中国海洋大学 Nanopore sequencing method for short-chain DNA
WO2024073278A1 (en) * 2022-09-26 2024-04-04 Illumina, Inc. Detecting and genotyping variable number tandem repeats

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8262900B2 (en) 2006-12-14 2012-09-11 Life Technologies Corporation Methods and apparatus for measuring analytes using large scale FET arrays
WO2013041577A1 (en) * 2011-09-20 2013-03-28 Vib Vzw Methods for the diagnosis of amyotrophic lateral sclerosis and frontotemporal lobar degeneration
CN104221022B (en) * 2012-04-05 2017-11-21 深圳华大基因股份有限公司 A kind of copy number mutation detection method and system
CN102766688B (en) * 2012-04-17 2014-04-02 盛司潼 Method for testing gene sequences
US9916416B2 (en) * 2012-10-18 2018-03-13 Virginia Tech Intellectual Properties, Inc. System and method for genotyping using informed error profiles
US11049587B2 (en) * 2013-10-18 2021-06-29 Seven Bridges Genomics Inc. Methods and systems for aligning sequences in the presence of repeating elements
ES2915399T3 (en) * 2014-09-12 2022-06-22 Illumina Cambridge Ltd Detection of repeat expansions with short-read sequencing data

Also Published As

Publication number Publication date
US20200335178A1 (en) 2020-10-22
AU2015314114B2 (en) 2021-01-21
AU2021202149B2 (en) 2023-03-02
EP4092680A1 (en) 2022-11-23
CN113362891A (en) 2021-09-07
DK3191993T3 (en) 2022-07-25
EP3191993B1 (en) 2022-04-20
PL3191993T3 (en) 2022-06-20
EP3191993A1 (en) 2017-07-19
US20170249421A1 (en) 2017-08-31
ES2915399T3 (en) 2022-06-22
US10699801B2 (en) 2020-06-30
LT3191993T (en) 2022-05-25
CN107077537A (en) 2017-08-18
CN107077537B (en) 2021-06-22
WO2016038220A1 (en) 2016-03-17
AU2021202149A1 (en) 2021-05-06
PT3191993T (en) 2022-06-20
AU2015314114A1 (en) 2017-03-30
AU2023203424B2 (en) 2025-05-29

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